BrukerTimsImagingFile.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
 
#ifdef WITH_OPENTIMS
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/FORMAT/BrukerTimsFile.h>
#include <OpenMS/IMAGING/MSImagingExperiment.h>
 
#include <memory>
#include <vector>
 
namespace OpenMS
{
  class TempDir;
 
  class OPENMS_DLLAPI BrukerTimsImagingFile : public ProgressLogger
  {
  public:
    struct MaldiPixel
    {
      Int frame_id = 0; 
      Int x = 0;        
      Int y = 0;        
    };
 
    struct Config
    {
      BrukerTimsFile::Config inner_config;
 
      bool strict_imaging_only = true;
    };
 
    BrukerTimsImagingFile() = default;
 
    void load(const std::string& path, MSImagingExperiment& exp);
 
    void load(const std::string& path, MSImagingExperiment& exp, const Config& config);
 
    static bool isImagingDataset(const std::string& path);
 
    static std::vector<MaldiPixel> readMaldiFrameInfo(const std::string& d_folder);
 
    static std::string readGlobalMetadataValue(const std::string& d_folder, const std::string& key);
 
  private:
    static void computeBoundingBox_(const std::vector<MaldiPixel>& rows,
                                    Int& x_min, Int& y_min,
                                    UInt& width, UInt& height);
 
    static std::string resolveTdfPath_(const std::string& path, std::unique_ptr<TempDir>& temp_dir);
  };
 
} // namespace OpenMS
 
#endif // WITH_OPENTIMS